Predicting protein-protein interactions between human and hepatitis C virus via an ensemble learning method

An estimated 170 million people, approximately 3% of the world population, are chronically infected with the hepatitis C virus (HCV). More than 350 000 deaths are reported annually, which are caused by HCV. HCV, similar to a variety of viruses, causes disease in humans by altering protein-protein interactions within the host cells. Experimental approaches for the detection of host-virus PPIs have many inherent limitations. Computational approaches to predict these interactions are therefore of significant importance. While many studies have been developed to predict intra-species PPIs in the last decade, predictions on inter-species PPIs such as human-HCV PPIs are rare. In this study, we developed an ensemble learning method to predict PPIs between human and HCV proteins. Our model utilises four well-established diverse learners as base classifiers including random forest (RF), Naive Bayes (NB), support vector machine (SVM) and multilayer perceptron (MLP). In addition, an MLP was used as a meta-learner to combine base learners' predictions to provide the final prediction. To encode human and HCV proteins as feature vectors, we used six different descriptors as follows: amino acid composition (ACC), pseudo amino acid composition (PAC), evolutionary information feature, network centrality measures, tissue information and post-translational modification information. To assess the prediction power of the proposed method, we assembled a benchmark dataset composed of confident positive and negative PPIs. In a 10-fold cross-validation experiment, our prediction method achieved accuracy and specificity as high as 83% and 94%, respectively. Furthermore, in an independent test set the proposed method achieved an accuracy of 84% and a specificity of 92%. When compared with the existing method, our method showed a better performance. These results revealed that our method is suitable for performing PPI prediction in a host-pathogen context.